GapMind for catabolism of small carbon sources

 

L-valine catabolism in Shewanella loihica PV-4

Best path

brnQ, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, prpC, acnD, prpF, acn, prpB

Also see fitness data for the top candidates

Rules

Overview: Valine degradation in GapMind is based on MetaCyc pathway L-valine degradation I (link). The other pathways do not produce any fixed carbon and are not included.

47 steps (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
brnQ L-valine:cation symporter BrnQ/BraZ/BraB Shew_0769
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit Shew_1925
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit Shew_1926 Shew_0901
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component Shew_1927 Shew_3430
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component Shew_3429 Shew_3660
acdH isobutyryl-CoA dehydrogenase Shew_1669 Shew_2570
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Shew_1670 Shew_0019
bch 3-hydroxyisobutyryl-CoA hydrolase Shew_1671
mmsB 3-hydroxyisobutyrate dehydrogenase Shew_1672 Shew_1609
mmsA methylmalonate-semialdehyde dehydrogenase Shew_1668 Shew_0965
prpC 2-methylcitrate synthase Shew_1821 Shew_1650
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Shew_1822
prpF methylaconitate isomerase Shew_1823
acn (2R,3S)-2-methylcitrate dehydratase Shew_1822 Shew_3424
prpB 2-methylisocitrate lyase Shew_1276 Shew_1820
Alternative steps:
Bap2 L-valine permease Bap2
bcaP L-valine uptake transporter BcaP/CitA
dddA 3-hydroxypropionate dehydrogenase
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase Shew_2425 Shew_1670
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Shew_0965 Shew_1668
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) Shew_2606 Shew_3310
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) Shew_2611 Shew_3310
livH L-valine ABC transporter, permease component 1 (LivH/BraD)
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-valine ABC transporter, permease component 2 (LivM/BraE) Shew_2608
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
natA L-valine ABC transporter, ATPase component 1 (NatA) Shew_2611 Shew_3310
natB L-valine ABC transporter, substrate-binding component NatB
natC L-valine ABC transporter, permease component 1 (NatC)
natD L-valine ABC transporter, permease component 2 (NatD) Shew_2609
natE L-valine ABC transporter, ATPase component 2 (NatE) Shew_2606 Shew_3164
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB
pccA propionyl-CoA carboxylase, alpha subunit Shew_2573 Shew_3365
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Shew_2573 Shew_3365
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit Shew_1220
pccB propionyl-CoA carboxylase, beta subunit Shew_2571 Shew_2867
pco propanyl-CoA oxidase Shew_0900
phtJ L-valine uptake permease PhtJ
prpD 2-methylcitrate dehydratase
vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB
vorC branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory